The response of the wave-driven circulation within coastally bounded reef-lagoon systems to varying lagoon and channel morphology was investigated using a two-dimensional coupled wave-circulation numerical model. Numerical experiments were conducted using a series of coastal reefs that incorporated a wide range of different lagoon depths and channel widths. With the morphology of both the reef (forereef and reef flat) and incident wave forcing held constant, the wave-driven circulation was found to increase substantially as dimensionless reef morphology parameters characterizing the relative lagoon depth and channel width were each independently increased. Analysis of the wave setup fields revealed that this increased flow was due to an enhancement of the cross-reef water level gradient, resulting from a sharp reduction in the lagoon setup as the frictional resistance on the lagoon-channel return flow was diminished. This follows similar trends observed in existing field and laboratory studies of wave-driven reef flows. Analysis of flushing time scales computed for each reef-lagoon geometry predicted the existence of optimal dimensionless lagoon depths and channel widths for a reef system, to establish maximal coastal flushing. Overall, the circulation and flushing of coastal reef-lagoon systems was found to be largely controlled by the particular morphology of the lagoon and channel region rather than solely by the morphology of the forereef and reef flat that has been the primary focus of analytical models developed to predict wave setup and circulation on reefs.